%% This is file `elsarticle-template-2-harv.tex',
%%
%% Copyright 2009 Elsevier Ltd
%%
%% This file is part of the 'Elsarticle Bundle'.
%% ---------------------------------------------
%%
%% It may be distributed under the conditions of the LaTeX Project Public
%% License, either version 1.2 of this license or (at your option) any
%% later version. The latest version of this license is in
%% http://www.latex-project.org/lppl.txt
%% and version 1.2 or later is part of all distributions of LaTeX
%% version 1999/12/01 or later.
%%
%% The list of all files belonging to the 'Elsarticle Bundle' is
%% given in the file `manifest.txt'.
%%
%% Template article for Elsevier's document class `elsarticle'
%% with harvard style bibliographic references
%%
%% $Id: elsarticle-template-2-harv.tex 155 2009-10-08 05:35:05Z rishi $
%% $URL: http://lenova.river-valley.com/svn/elsbst/trunk/elsarticle-template-2-harv.tex $
%%
\documentclass[preprint,authoryear,12pt]{elsarticle}

%% Use the option review to obtain double line spacing
%% \documentclass[authoryear,preprint,review,12pt]{elsarticle}

%% Use the options 1p,twocolumn; 3p; 3p,twocolumn; 5p; or 5p,twocolumn
%% for a journal layout:
%% \documentclass[final,authoryear,1p,times]{elsarticle}
%% \documentclass[final,authoryear,1p,times,twocolumn]{elsarticle}
%% \documentclass[final,authoryear,3p,times]{elsarticle}
%% \documentclass[final,authoryear,3p,times,twocolumn]{elsarticle}
%% \documentclass[final,authoryear,5p,times]{elsarticle}
%% \documentclass[final,authoryear,5p,times,twocolumn]{elsarticle}

%% if you use PostScript figures in your article
%% use the graphics package for simple commands
%% \usepackage{graphics}
%% or use the graphicx package for more complicated commands
%% \usepackage{graphicx}
%% or use the epsfig package if you prefer to use the old commands
%% \usepackage{epsfig}

%% The amssymb package provides various useful mathematical symbols
\usepackage{amssymb}
%% The amsthm package provides extended theorem environments
%% \usepackage{amsthm}

%% The lineno packages adds line numbers. Start line numbering with
%% \begin{linenumbers}, end it with \end{linenumbers}. Or switch it on
%% for the whole article with \linenumbers after \end{frontmatter}.
%\usepackage{lineno}

%% natbib.sty is loaded by default. However, natbib options can be
%% provided with \biboptions{...} command. Following options are
%% valid:

%% round - round parentheses are used (default)
%% square - square brackets are used [option]
%% curly - curly braces are used {option}
%% angle - angle brackets are used <option>
%% semicolon - multiple citations separated by semi-colon (default)
%% colon - same as semicolon, an earlier confusion
%% comma - separated by comma
%% authoryear - selects author-year citations (default)
%% numbers- selects numerical citations
%% super - numerical citations as superscripts
%% sort - sorts multiple citations according to order in ref. list
%% sort&compress - like sort, but also compresses numerical citations
%% compress - compresses without sorting
%% longnamesfirst - makes first citation full author list
%%
%% \biboptions{longnamesfirst,comma}

% \biboptions{}

\usepackage[authoryear]{natbib}

\usepackage{subfigure}


\journal{Journal of Applied Ecology}

\begin{document}

\begin{frontmatter}

%% Title, authors and addresses

%% use the tnoteref command within \title for footnotes;
%% use the tnotetext command for the associated footnote;
%% use the fnref command within \author or \address for footnotes;
%% use the fntext command for the associated footnote;
%% use the corref command within \author for corresponding author footnotes;
%% use the cortext command for the associated footnote;
%% use the ead command for the email address,
%% and the form \ead[url] for the home page:
%%
%% \title{Title\tnoteref{label1}}
%% \tnotetext[label1]{}
%% \author{Name\corref{cor1}\fnref{label2}}
%% \ead{email address}
%% \ead[url]{home page}
%% \fntext[label2]{}
%% \cortext[cor1]{}
%% \address{Address\fnref{label3}}
%% \fntext[label3]{}

\title{The art of CPUE. Making use of fisheries dependant indices of abundance in a meaningful way}

%% use optional labels to link authors explicitly to addresses:
\author[label1]{Paul de Bruyn, Laurence T. Kell} 
%% \address[label1]{<address>}
%% \address[label2]{<address>}

%\author{Paul de Bruyn, Laurence T. Kell \\
 % $^1$ International Commission for the Conservation of Atlantic Tunas (ICCAT)} %,C/Corazo´n de Marı´a, 8, 28002 Madrid, Spain} \date{Received 1998 December 18; in original form 1998 November 22}


\address{}

\begin{abstract}
%% Text of abstract

CPUE are used for etc etc etc...

\end{abstract}

\begin{keyword}
%% keywords here, in the form: keyword \sep keyword

%% MSC codes here, in the form: \MSC code \sep code
%% or \MSC[2008] code \sep code (2000 is the default)

A list in alphabetical order not exceeding ten words or short phrases, excluding words used in the title and chosen carefully to reflect the precise content of the paper.

\end{keyword}

\end{frontmatter}

\newpage
\tableofcontents
\newpage

%\linenumbers

%% main text

\section{Outline} 

\section{Introduction} Stock assessments are routinely conducted for tuna and other highly migratory species managed by  
the International Commission for the Conservation of Atlantic Tuna (ICCAT). Such species rarely have fisheries independant 
sources of data on stock abundance, therefore catch per unit effort (CPUE) indices derived from the fisheries are 
used as proxies for abundance. Although population dynamics models often assume that CPUE is proportional to
abundance, analysts have long been aware that CPUE series may not accurately reflect abundance \citep{beverton1993dynamics}, \citep{harley2001catch}.
Factors such as changes in the spatial distribution of populations and the allocation of effort in response to
managed and economic conditions all affect catches and effort in relation to stock abundance \citep{paloheimo1964abundance}, \citep{tidd2011exit}.

ICCAT has developed protocols used to assess the quality of an individual CPUE index. We discuss these
protocol and the potential consequences for stock assessment and management advice consistent with the Precautionary Approach \citep{Garcia1996}.
For example do the protocols
 
 \begin{itemize}
 \item help to understand a particular CPUE series, i.e. changes in targeting that may make it invalid as proxy for stock abundance
 \item help to understand the cause of any conflicting trends between indices.
 \item identify the limitations of an index which may render them meaningless as indices of abundance
 \item allow scorings to be developed that allow  CPUE series to be assigned weights in assessment models
 \item allow hypothesis about the state of a stock based on CPUE series with conflicting trends to be developed
\end{itemize}
  

\section{Materials and methods} 

ICCAT has developed protocols for assessing CPUEs. These are intended to evaluate the suitability of CPUE indices 
for inclusion in stock assessments. ICCAT developed two tools. The first is a flowchart that is intended to guide the 
appropriate use of CPUE series in a particular stock assessment models given the model assumptions. The flowchart 
is intended to be used prior to the construction of stock assessment models to ensure that CPUE series 
used in a stock assessment model (e.g. in biomass dynamic, age-structured, spatial models) actually conform to the 
assumptions. 

The second tool is a table intended to evaluate the sufficiency of CPUE series, and inform decisions regarding 
their inclusion in stock assessment models. The idea is to stimulate discussion regarding the strengths and limitations of each 
series and thus how they can most effectively be utilised and in which circumstances.

\subsection{Description of Data Prep Meeting} 

Basically CPCs produce CPUE from confidential disaggregated data sets. Task I and II data sets held by ICCAT are used when these stes are not available. The group reviews theses indices and makes judgments as to whther they should be used, and in what models. The judgements are often subjective. The protocols prescribed by the ICCAT methods working group are being refined and modified to reduce the subjectivity but this needs to be further improved as the protocols are guidelines and are time consuming bearing in mind the extremely limited time available during data preparatory meetings. CPUEs are not actually scored or weighted, but rather discussed and considered. 

\subsection{Description of Stock Assessment Meeting} 

During ICCAT assessment sessions, a variety of assessment models are used. As CPUEs often show very different trends, several scenarios are considered for each run. An impartial system for analysising the plausibility of the different scenarios would be beneficial, where there is sufficient information to be able to do so quantitatively.

\section{Results} 

\textit{}

In this section we present some examples of the protocols and some quantitive analyses based upon them

\subsection{Protocols} 

\begin{itemize}
 \item Example of the flowchart
 \item Example of the scorings
\end{itemize}
 
\subsection{Spatial Indices} 

CPUE time series may be affected by a variety of factors, indices such as the Gulland and Gini may help 
to identify patterns due to targeting \citep{mckechnie2013longline}. 
  
\subsection{Likelihood profiles}

Often the CPUE indices used when fitting an assessment model are conflicting and produces parameter estimates intermediate 
to what would be obtained from the data sets individually. 
However, the most likely parameter values are not intermediary but are more likely to occur at one of 
the apparent extremes \citep{schnute1993analysis}. We therefore calculating likelihood profiles by data component (i.e.
each index) for key parameter such as carrying capacity ($K$) and maximum sustainable yield ($MSY$).
 

\section{Discussion} 
\textit{}

 
 \begin{itemize}
 \item Use of protocols to fully investigate and understand CPUE series. Their strengths and limitations
 \item Use of possible scorings to rank CPUEs and possibly to weight them in assessment models
 \item Recognising the limitations of different series, particularly in the light of management actions which render CPUEs meaningless as indices of abundance (eg. BFT)
 \item Understanding why and in what circumstances CPUE series for the same stocks may have different and in some cases completely conflicting trends.
 \item Formulating and investigating different hypothesis about the state of a stock based on CPUE series with conflicting trends.
 \item Evaluating the implications on magament advice for these different hypothesis (eg, MSE framework)
\end{itemize}

\section{Acknowledgements} 

\textit{[Be brief. If authors refer to themselves as recipients of assistance or funding, they should do so by their 
initials separated by points (e.g. J.B.T.). Do not acknowledge Editors by name.]}

\section{Data Accessibility} 
\textit{[To enable readers to locate archived data from papers, we require that authors list the database and 
the respective accession numbers or DOIs for all data from the manuscript that has been made publicly available. 
An example of what this section should look like can be found in the Data Archiving Q\&A.}]

\section{Supporting Information} 

\textit{[Essential supporting information can be published in the online version of the article. 
Instructions for the preparation of Supporting Information are given here and general guidance is available here.]}


%% The Appendices part is started with the command \appendix;
%% appendix sections are then done as normal sections
%% \appendix

%% \section{}
%% \label{}
%% References
%%
%% Following citation commands can be used in the body text:
%%
%% \citet{key} ==>> Jones et al. (1990)
%% \citep{key} ==>> (Jones et al., 1990)
%%
%% Multiple citations as normal:
%% \citep{key1,key2} ==>> (Jones et al., 1990; Smith, 1989)
%%  or (Jones et al., 1990, 1991)
%%  or (Jones et al., 1990a,b)
%% \citep{key} is the equivalent of \citet{key} in author-year mode
%%
%% Full author lists may be forced with \citet* or \citep*, e.g.
%% \citep*{key} ==>> (Jones, Baker, and Williams, 1990)
%%
%% Optional notes as:
%% \citep[chap. 2]{key} ==>> (Jones et al., 1990, chap. 2)
%% \citep[e.g.,][]{key} ==>> (e.g., Jones et al., 1990)
%% \citep[see][pg. 34]{key}==>> (see Jones et al., 1990, pg. 34)
%% (Note: in standard LaTeX, only one note is allowed, after the ref.
%% Here, one note is like the standard, two make pre- and post-notes.)
%%
%% \citealt{key} ==>> Jones et al. 1990
%% \citealt*{key} ==>> Jones, Baker, and Williams 1990
%% \citealp{key} ==>> Jones et al., 1990
%% \citealp*{key} ==>> Jones, Baker, and Williams, 1990
%%
%% Additional citation possibilities
%% \citeauthor{key} ==>> Jones et al.
%% \citeauthor*{key} ==>> Jones, Baker, and Williams
%% \citeyear{key} ==>> 1990
%% \citeyearpar{key} ==>> (1990)
%% \citetext{priv. comm.} ==>> (priv. comm.)
%% \citenum{key} ==>> 11 [non-superscripted]
%% Note: full author lists depends on whether the bib style supports them;
%% if not, the abbreviated list is printed even when full requested.
%%
%% For names like della Robbia at the start of a sentence, use
%% \Citet{dRob98} ==>> Della Robbia (1998)
%% \Citep{dRob98} ==>> (Della Robbia, 1998)
%% \Citeauthor{dRob98} ==>> Della Robbia


%% References with bibTeX database:

\newpage\clearpage

\bibliography{/home/laurie/Desktop/scrs2014/include/tex/refs}
%C:/Users/pdebruyn/Documents/SCRS2014/include/tex/refs}
%\bibliographystyle{model2-names}
\bibliographystyle{abbrvnat} 

%% Authors are advised to submit their bibtex database files. They are
%% requested to list a bibtex style file in the manuscript if they do
%% not want to use model2-names.bst.

%% References without bibTeX database:

% \begin{thebibliography}{00}

%% \bibitem must have one of the following forms:
%% \bibitem[Jones et al.(1990)]{key}...
%% \bibitem[Jones et al.(1990)Jones, Baker, and Williams]{key}...
%% \bibitem[Jones et al., 1990]{key}...
%% \bibitem[\protect\citeauthoryear{Jones, Baker, and Williams}{Jones
%% et al.}{1990}]{key}...
%% \bibitem[\protect\citeauthoryear{Jones et al.}{1990}]{key}...
%% \bibitem[\protect\astroncite{Jones et al.}{1990}]{key}...
%% \bibitem[\protect\citename{Jones et al., }1990]{key}...
%% \harvarditem[Jones et al.]{Jones, Baker, and Williams}{1990}{key}...
%%

% \bibitem[ ()]{}

% \end{thebibliography}


%FAO 1 © 2005-2012. World inventory of fisheries. Precautionary approach to fisheries management. Issues Fact Sheets. Text by Serge M. Garcia. In: FAO Fisheries and Aquaculture Department [online]. Rome. Updated 27 May 2005. [Cited 19 August 2012]. http://www.fao.org/fishery/topic/13302/en
%FAO 2 © 2005-2012. Fisheries and Aquaculture topics. The ecosystem approach to fisheries management. Topics Fact Sheets. Text by S.M. Garcia and K.L. Cochrane. In: FAO Fisheries and Aquaculture Department [online]. Rome. Updated 27 May 2005. [Cited 19 August 2012]. http://www.fao.org/fishery/topic/13261/en
%FAO 1996 Precautionary approach to capture fisheries and species introductions. Elaborated by the Technical Consultation on the Precautionary Approach to Capture Fisheries (Including Species Introductions). Lysekil, Sweden, 6-13 June 1995. FAO Technical Guidelines for Responsible Fisheries. No. 2. FAO, Rome.
%United Nations 1995. Agreement for the implementation of the provisions of the United Nations Convention on the Law of the Sea of 10 December 1982 relating to the Conservation and Management of Straddling Fish Stocks and Highly Migratory Fish Stocks. 4 December 1995. UN Doc. A/Conf. 164/37.


\clearpage\newpage
\section{Tables}

Tables (see Specifications). Each table should be on a separate page, numbered and accompanied by a legend at the top. These should be referred to in the text as Table 1, etc. Avoid duplication between figures and tables.


\clearpage\newpage
\section{Figures}


Figures (see Specifications). Figures and their legends should be grouped together at the end of the paper before Supporting Information (if present). If figures have been supplied as a list at the end of the text file (as recommended), they should appear above their respective legend. Figures should be referred to in the text as Fig. 1, Figs 1 \& 2, etc. Photographic material should also be referred to as Figures. Do not include high-resolution versions of figures at submission; reduce the size and resolution of graphics to a file size of less than 1 MB. If a manuscript is accepted, higher quality versions of figures can be submitted at a later stage.

%\begin{figure}[htbp]
%\begin{figure}
%\includegraphics[width=6in]{3s-stars4.png}
%\caption{$SPR_{F=0}$ by cohort Sequential t test for regime shifts (Rodionov, 2004)}
%\label{regime4}\end{figure}

\end{document}




 